use AppConfig initializer with file parameter

server/common/config/app_config.py

@@ -1,4 +1,6 @@
 import copy
+import logging
+
 import yaml
 from flatten_dict import unflatten as _unflatten, flatten as _flatten
 
@@ -18,9 +20,8 @@ def unflatten(dictionary: dict) -> dict:
 class AppConfig(object):
     """
     AppConfig stores all the configuration for cellxgene.
-    AppConfig contains one or more DatasetConfig(s) and one ServerConfig.
-    The server_config contains attributes that refer to the server process as a whole.
-    The default_dataset_config refers to attributes that are associated with the features and
+    The self.server contains attributes that refer to the server process as a whole.
+    The self.default_dataset refers to attributes that are associated with the features and
     presentations of a dataset.
     The dataset config attributes can be overridden depending on the url by which the
     dataset was accessed.  These are stored in dataroot_config.
@@ -33,6 +34,7 @@ def __init__(self, config_file_path: str = None):
         self.default_config: dict = get_default_config()
         self.config: dict = copy.deepcopy(self.default_config)
         self.valid = False
+        self.dataroot_config = {}
         if config_file_path:
             self.update_from_config_file(config_file_path)
 
@@ -83,6 +85,7 @@ def update_config(self, **kw):
         )
         for value in self.dataroot_config.values():
             value = value.update(**new_config["default_dataset"])
+        logging.info("Configuration updated")
 
     def _open_config_file(self, config_file: str):
         try:
@@ -115,6 +118,7 @@ def complete_config(self):
             self.config = self.validate_config(self.config)
         self.handle_adaptor()
         self.handle_data_source()
+        logging.info("Configuration complete.")
 
     def get_dataset_config(self, dataroot_key: str) -> dict:
         return self.dataroot_config.get(dataroot_key, self.default_dataset)

server/ecs/app.py

@@ -140,18 +140,14 @@ def get_csp_hashes(app, app_config):
 
 
 try:
-    app_config = AppConfig()
-
-    has_config = False
+    app_config = False
     # config file: look first for "config.yaml" in the current working directory
     config_file = "config.yaml"
     config_location = DataLocator(config_file)
     if config_location.exists():
         with config_location.local_handle() as lh:
             logging.info(f"Configuration from {config_file}")
-            app_config.update_from_config_file(lh)
-            has_config = True
-
+            app_config = AppConfig(lh)
     else:
         # config file: second, use the CXG_CONFIG_FILE
         config_file = os.getenv("CXG_CONFIG_FILE")
@@ -161,13 +157,12 @@ def get_csp_hashes(app, app_config):
             if config_location.exists():
                 with config_location.local_handle() as lh:
                     logging.info(f"Configuration from {config_file}")
-                    app_config.update_from_config_file(lh)
-                    has_config = True
+                    app_config = AppConfig(lh)
             else:
                 logging.critical(f"Configuration file not found {config_file}")
                 sys.exit(1)
 
-    if not has_config:
+    if not app_config:
         logging.critical("No config file found")
         sys.exit(1)
 
@@ -177,7 +172,7 @@ def get_csp_hashes(app, app_config):
         app_config.update_server_config(multi_dataset__dataroot=dataroot)
 
     # complete config
-    app_config.complete_config(logging.info)
+    app_config.complete_config()
 
     server = WSGIServer(app_config)
     debug = False

server/tests/unit/common/config/test_app_config.py

@@ -22,8 +22,7 @@ def get_config(self, **kwargs):
         file_name = self.custom_app_config(
             dataroot=f"{FIXTURES_ROOT}", config_file_name=self.config_file_name, **kwargs
         )
-        config = AppConfig()
-        config.update_from_config_file(file_name)
+        config = AppConfig(file_name)
         return config
 
     def test_get_default_config_correctly_reads_default_config_file(self):
@@ -82,8 +81,7 @@ def test_configfile_no_dataset_section(self):
                 """
                 fconfig.write(config)
 
-            app_config = AppConfig()
-            app_config.update_from_config_file(configfile)
+            app_config = AppConfig(configfile)
             server_changes = self.compare_configs(app_config, default_config)
             self.assertCountEqual(
                 server_changes,
@@ -106,8 +104,7 @@ def test_configfile_no_server_section(self):
                 """
                 fconfig.write(config)
 
-            app_config = AppConfig()
-            app_config.update_from_config_file(configfile)
+            app_config = AppConfig(configfile)
             changes = self.compare_configs(app_config, default_config)
             self.assertCountEqual(changes, [('default_dataset__app__about_legal_tos', 'expected_value', None),
                                             ('server__app__port', 5005, None),

server/tests/unit/common/config/test_base_config.py

@@ -25,8 +25,7 @@ def get_config(self, **kwargs):
         file_name = self.custom_app_config(
             config_file_name=self.config_file_name, **kwargs
         )
-        config = AppConfig()
-        config.update_from_config_file(file_name)
+        config = AppConfig(file_name)
         return config
 
     def test_mapping_creation_returns_map_of_server_and_dataset_config(self):

server/tests/unit/common/config/test_dataset_config.py

@@ -127,9 +127,7 @@ def test_configfile_with_specialization(self):
 
                 """
                 fconfig.write(config)
-
-            app_config = AppConfig()
-            app_config.update_from_config_file(configfile)
+            app_config = AppConfig(configfile)
 
             # test config from specialization
             self.assertEqual(app_config.server__multi_dataset__dataroots["test"]["base_url"], "test")

server/tests/unit/common/config/test_server_config.py

@@ -32,8 +32,7 @@ def get_config(self, **kwargs):
         file_name = self.custom_app_config(
             dataroot=f"{FIXTURES_ROOT}", config_file_name=self.config_file_name, **kwargs
         )
-        config = AppConfig()
-        config.update_from_config_file(file_name)
+        config = AppConfig(file_name)
         return config
 
     def test_init_raises_error_if_default_config_is_invalid(self):
@@ -60,9 +59,8 @@ def test_handle_data_locator_works_for_default_types(self, mock_discover_region_
         file_name = self.custom_app_config(
             dataroots=dataroots, config_file_name=self.config_file_name, data_locator_region_name="true"
         )
-        config = AppConfig()
         with self.assertRaises(ConfigurationError):
-            config.update_from_config_file(file_name)
+            config = AppConfig(file_name)
 
     @patch("server.common.config.config_model.discover_s3_region_name")
     def test_handle_data_locator_can_read_from_dataroot(self, mock_discover_region_name):
@@ -74,8 +72,7 @@ def test_handle_data_locator_can_read_from_dataroot(self, mock_discover_region_n
         file_name = self.custom_app_config(
             dataroots=dataroots, config_file_name=self.config_file_name, data_locator_region_name="true"
         )
-        config = AppConfig()
-        config.update_from_config_file(file_name)
+        config = AppConfig(file_name)
         self.assertEqual(config.server__data_locator__s3_region_name, "us-west-2")
         mock_discover_region_name.assert_called_once_with("s3://hosted-cellxgene-dev")
 
@@ -90,8 +87,7 @@ def test_handle_data_source__errors_when_passed_zero(self):
         )
 
         file_name = self.custom_app_config(config_file_name="zero_roots.yml")
-        config = AppConfig()
-        config.update_from_config_file(file_name)
+        config = AppConfig(file_name)
         with self.subTest("zero roots"):
             with self.assertRaises(ConfigurationError):
                 config.handle_data_source()
@@ -221,8 +217,7 @@ def test_handle_adaptor(self, mock_tiledb_context):
             cxg_tile_cache_size=10,
             cxg_tiledb_py_init_buffer_size=10,
         )
-        config = AppConfig()
-        config.update_from_config_file(custom_config)
+        config = AppConfig(custom_config)
         config.handle_adaptor()
         mock_tiledb_context.assert_called_once_with(
             {